From 0259f0fde8d4abfb7f7bfc72ec7fc707117d2dda Mon Sep 17 00:00:00 2001 From: Alexander Berger Date: Wed, 23 Oct 2024 14:11:40 -0400 Subject: [PATCH 1/9] Update version and dependencies --- poetry.lock | 45 +++++++++++++++++++++++++++++++-------------- pyproject.toml | 7 ++++--- 2 files changed, 35 insertions(+), 17 deletions(-) diff --git a/poetry.lock b/poetry.lock index d1dbe75..d6c302c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -509,13 +509,13 @@ test = ["pytest (>=6)"] [[package]] name = "fastapi" -version = "0.115.0" +version = "0.115.3" description = "FastAPI framework, high performance, easy to learn, fast to code, ready for production" optional = false python-versions = ">=3.8" files = [ - {file = "fastapi-0.115.0-py3-none-any.whl", hash = "sha256:17ea427674467486e997206a5ab25760f6b09e069f099b96f5b55a32fb6f1631"}, - {file = "fastapi-0.115.0.tar.gz", hash = "sha256:f93b4ca3529a8ebc6fc3fcf710e5efa8de3df9b41570958abf1d97d843138004"}, + {file = "fastapi-0.115.3-py3-none-any.whl", hash = "sha256:8035e8f9a2b0aa89cea03b6c77721178ed5358e1aea4cd8570d9466895c0638c"}, + {file = "fastapi-0.115.3.tar.gz", hash = "sha256:c091c6a35599c036d676fa24bd4a6e19fa30058d93d950216cdc672881f6f7db"}, ] [package.dependencies] @@ -530,7 +530,7 @@ pydantic-extra-types = {version = ">=2.0.0", optional = true, markers = "extra = pydantic-settings = {version = ">=2.0.0", optional = true, markers = "extra == \"all\""} python-multipart = {version = ">=0.0.7", optional = true, markers = "extra == \"all\""} pyyaml = {version = ">=5.3.1", optional = true, markers = "extra == \"all\""} -starlette = ">=0.37.2,<0.39.0" +starlette = ">=0.40.0,<0.42.0" typing-extensions = ">=4.8.0" ujson = {version = ">=4.0.1,<4.0.2 || >4.0.2,<4.1.0 || >4.1.0,<4.2.0 || >4.2.0,<4.3.0 || >4.3.0,<5.0.0 || >5.0.0,<5.1.0 || >5.1.0", optional = true, markers = "extra == \"all\""} uvicorn = {version = ">=0.12.0", extras = ["standard"], optional = true, markers = "extra == \"all\""} @@ -578,13 +578,13 @@ requests = ">=2.32.0,<3.0.0" [[package]] name = "geneweaver-db" -version = "0.5.0" +version = "0.6.0a0" description = "Database Interaction Services for GeneWeaver" optional = false python-versions = "<4.0,>=3.9" files = [ - {file = "geneweaver_db-0.5.0-py3-none-any.whl", hash = "sha256:7bb40b7a50783a48092ddf6529aca70c49bfb69da6e52420076cc300769db297"}, - {file = "geneweaver_db-0.5.0.tar.gz", hash = "sha256:170ee8fdc7efe5f3a6989014db0b6e2c02d9da3ff8b085ca218168f3cfcc8d21"}, + {file = "geneweaver_db-0.6.0a0-py3-none-any.whl", hash = "sha256:7d69abbc26b100337935da9bf7255877a42c6f86a6265b5e70b828140040c1c6"}, + {file = "geneweaver_db-0.6.0a0.tar.gz", hash = "sha256:5bb7bfce5c3f1556c4d6779090f0e8e46905c740ca510af3d0556660b1038d85"}, ] [package.dependencies] @@ -767,6 +767,23 @@ files = [ {file = "itsdangerous-2.2.0.tar.gz", hash = "sha256:e0050c0b7da1eea53ffaf149c0cfbb5c6e2e2b69c4bef22c81fa6eb73e5f6173"}, ] +[[package]] +name = "jax-apiutils" +version = "0.1.0a6" +description = "Utilities to simplify API development." +optional = false +python-versions = "<4.0,>=3.9" +files = [ + {file = "jax_apiutils-0.1.0a6-py3-none-any.whl", hash = "sha256:f8c75ae0fba4fa58cbc25e56fd168fecd0b1ad9fbe6630082a12bd9f23f1dfe1"}, + {file = "jax_apiutils-0.1.0a6.tar.gz", hash = "sha256:0293166f0deefdf358aac910ccb1cc47729102907f769e4b34a79039000eacb6"}, +] + +[package.extras] +all = ["fastapi (>=0.100.0)", "pydantic (>=2.0.0)", "pyjwt (>=2.9.0,<3.0.0)", "requests (>=2.32.3,<3.0.0)"] +fastapi = ["fastapi (>=0.100.0)"] +jwt = ["pyjwt (>=2.9.0,<3.0.0)", "requests (>=2.32.3,<3.0.0)"] +schemas = ["pydantic (>=2.0.0)"] + [[package]] name = "jinja2" version = "3.1.4" @@ -1509,13 +1526,13 @@ semver = ["semver (>=3.0.2)"] [[package]] name = "pydantic-settings" -version = "2.5.2" +version = "2.6.0" description = "Settings management using Pydantic" optional = false python-versions = ">=3.8" files = [ - {file = "pydantic_settings-2.5.2-py3-none-any.whl", hash = "sha256:2c912e55fd5794a59bf8c832b9de832dcfdf4778d79ff79b708744eed499a907"}, - {file = "pydantic_settings-2.5.2.tar.gz", hash = "sha256:f90b139682bee4d2065273d5185d71d37ea46cfe57e1b5ae184fc6a0b2484ca0"}, + {file = "pydantic_settings-2.6.0-py3-none-any.whl", hash = "sha256:4a819166f119b74d7f8c765196b165f95cc7487ce58ea27dec8a5a26be0970e0"}, + {file = "pydantic_settings-2.6.0.tar.gz", hash = "sha256:44a1804abffac9e6a30372bb45f6cafab945ef5af25e66b1c634c01dd39e0188"}, ] [package.dependencies] @@ -1865,13 +1882,13 @@ files = [ [[package]] name = "starlette" -version = "0.38.6" +version = "0.41.0" description = "The little ASGI library that shines." optional = false python-versions = ">=3.8" files = [ - {file = "starlette-0.38.6-py3-none-any.whl", hash = "sha256:4517a1409e2e73ee4951214ba012052b9e16f60e90d73cfb06192c19203bbb05"}, - {file = "starlette-0.38.6.tar.gz", hash = "sha256:863a1588f5574e70a821dadefb41e4881ea451a47a3cd1b4df359d4ffefe5ead"}, + {file = "starlette-0.41.0-py3-none-any.whl", hash = "sha256:a0193a3c413ebc9c78bff1c3546a45bb8c8bcb4a84cae8747d650a65bd37210a"}, + {file = "starlette-0.41.0.tar.gz", hash = "sha256:39cbd8768b107d68bfe1ff1672b38a2c38b49777de46d2a592841d58e3bf7c2a"}, ] [package.dependencies] @@ -2298,4 +2315,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "f8a520654164fa98985e67286dcb7e2dbeb86807811255902b321f22a1358fbb" +content-hash = "a809555b03e0e7b6998234f60ac3d533584482b122fd1d7a50ab9eac74ee665d" diff --git a/pyproject.toml b/pyproject.toml index 436f1af..b2ac91c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "geneweaver-api" -version = "0.10.0" +version = "0.11.0a0" description = "The Geneweaver API" authors = [ "Alexander Berger ", @@ -20,12 +20,13 @@ python = "^3.9" geneweaver-core = "^0.10.0a3" fastapi = {extras = ["all"], version = "^0.115.0"} uvicorn = {extras = ["standard"], version = "^0.30.0"} -geneweaver-db = "^0.5.0" +geneweaver-db = "^0.6.0a0" psycopg-pool = "^3.1.7" requests = "^2.32.3" python-jose = {extras = ["cryptography"], version = "^3.3.0"} psycopg-binary = "3.1.18" pydantic-settings = "^2.3.4" +jax-apiutils = "^0.1.0a6" [tool.poetry.group.dev.dependencies] geneweaver-testing = "^0.1.2" @@ -45,4 +46,4 @@ build-backend = "poetry.core.masonry.api" # TODO: Remove this when batch API is hooked up and tested. [tool.coverage.report] -omit = ["*/batch.py"] \ No newline at end of file +omit = ["*/batch.py"] From 6590f1e444a88ce516db91068d3497d3988a616f Mon Sep 17 00:00:00 2001 From: Alexander Berger Date: Wed, 23 Oct 2024 14:12:37 -0400 Subject: [PATCH 2/9] Update geneset endpoints and services for public usage --- src/geneweaver/api/controller/genesets.py | 27 ++++++++------ src/geneweaver/api/services/geneset.py | 44 +++++++++++------------ 2 files changed, 38 insertions(+), 33 deletions(-) diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py index 33d36fe..d0a8787 100644 --- a/src/geneweaver/api/controller/genesets.py +++ b/src/geneweaver/api/controller/genesets.py @@ -5,10 +5,10 @@ from tempfile import TemporaryDirectory from typing import Optional, Set -from fastapi import APIRouter, Depends, HTTPException, Path, Query, Security +from fastapi import APIRouter, Depends, HTTPException, Path, Query, Security, Request from fastapi.responses import FileResponse, StreamingResponse from geneweaver.api import dependencies as deps -from geneweaver.api.schemas.apimodels import GeneValueReturn, SearchResponse +from geneweaver.api.schemas.apimodels import GeneValueReturn from geneweaver.api.schemas.auth import UserInternal from geneweaver.api.schemas.search import GenesetSearch from geneweaver.api.services import geneset as genset_service @@ -18,6 +18,8 @@ from geneweaver.db import search as db_search from typing_extensions import Annotated +from jax.apiutils import CollectionResponse + from . import message as api_message router = APIRouter(prefix="/genesets", tags=["genesets"]) @@ -151,17 +153,20 @@ def get_visible_genesets( @router.get("/search") def search( + request: Request, geneset_search: Annotated[GenesetSearch, Query()], user: UserInternal = Security(deps.optional_full_user), cursor: Optional[deps.Cursor] = Depends(deps.cursor), -) -> SearchResponse: +) -> CollectionResponse: """Search genesets.""" - return SearchResponse( + return CollectionResponse( db_search.genesets( cursor, is_readable_by=0 if user is None else user.id, **geneset_search.model_dump(exclude_none=True), - ) + ), + url=request.url_for("search"), + **geneset_search.model_dump(exclude_none=True), ) @@ -170,7 +175,7 @@ def get_geneset( geneset_id: Annotated[ int, Path(format="int64", minimum=0, maxiumum=9223372036854775807) ], - user: UserInternal = Security(deps.full_user), + user: deps.OptionalFullUserDep, cursor: Optional[deps.Cursor] = Depends(deps.cursor), gene_id_type: Optional[GeneIdentifier] = None, in_threshold: Optional[bool] = None, @@ -199,7 +204,7 @@ def get_geneset_values( geneset_id: Annotated[ int, Path(format="int64", minimum=0, maxiumum=9223372036854775807) ], - user: UserInternal = Security(deps.full_user), + user: deps.OptionalFullUserDep, cursor: Optional[deps.Cursor] = Depends(deps.cursor), gene_id_type: Optional[GeneIdentifier] = None, in_threshold: Optional[bool] = None, @@ -232,7 +237,7 @@ def get_export_geneset_by_id_type( geneset_id: Annotated[ int, Path(format="int64", minimum=0, maxiumum=9223372036854775807) ], - user: UserInternal = Security(deps.full_user), + user: deps.OptionalFullUserDep, cursor: Optional[deps.Cursor] = Depends(deps.cursor), temp_dir: TemporaryDirectory = Depends(deps.get_temp_dir), gene_id_type: Optional[GeneIdentifier] = None, @@ -283,7 +288,7 @@ def get_geneset_metadata( geneset_id: Annotated[ int, Path(format="int64", minimum=0, maxiumum=9223372036854775807) ], - user: UserInternal = Security(deps.full_user), + user: deps.OptionalFullUserDep, cursor: Optional[deps.Cursor] = Depends(deps.cursor), include_pub_info: Optional[bool] = False, ) -> dict: @@ -306,7 +311,7 @@ def get_publication_for_geneset( geneset_id: Annotated[ int, Path(format="int64", minimum=0, maxiumum=9223372036854775807) ], - user: UserInternal = Security(deps.full_user), + user: deps.OptionalFullUserDep, cursor: Optional[deps.Cursor] = Depends(deps.cursor), ) -> dict: """Get the publication associated with the geneset.""" @@ -358,7 +363,7 @@ def get_geneset_ontology_terms( geneset_id: Annotated[ int, Path(format="int64", minimum=0, maxiumum=9223372036854775807) ], - user: UserInternal = Security(deps.full_user), + user: deps.OptionalFullUserDep, cursor: Optional[deps.Cursor] = Depends(deps.cursor), limit: Annotated[ Optional[int], diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py index 391d82e..3ee02e2 100644 --- a/src/geneweaver/api/services/geneset.py +++ b/src/geneweaver/api/services/geneset.py @@ -19,6 +19,17 @@ ONTO_GSO_REF_TYPE = "GeneWeaver Primary Annotation" +def determine_user_id(user: Optional[User] = None): + """Determine the user ID from the user object. + + :param user: The user object. + :return: The user ID. + """ + if user is None or user.id is None: + return 0 + return user.id + + def determine_geneset_access( user: Optional[User] = None, curation_tier: Optional[Set[GenesetTier]] = None, @@ -36,9 +47,10 @@ def determine_geneset_access( is_readable_by = None if user_is_none: - curation_tier = determine_public_geneset_curation_tier(curation_tier) if only_my_genesets: raise UnauthorizedException() + curation_tier = determine_public_geneset_curation_tier(curation_tier) + is_readable_by = 0 else: is_readable_by = user.id if only_my_genesets: @@ -178,12 +190,9 @@ def get_geneset_metadata( @return: dictionary response (geneset). """ try: - if user is None or user.id is None: - return {"error": True, "message": message.ACCESS_FORBIDDEN} - results = db_geneset.get( cursor, - is_readable_by=user.id, + is_readable_by=determine_user_id(user), gs_id=geneset_id, with_publication_info=include_pub_info, ) @@ -206,12 +215,9 @@ def get_geneset( @return: dictionary response (geneset and genset values). """ try: - if user is None or user.id is None: - return {"error": True, "message": message.ACCESS_FORBIDDEN} - results = db_geneset.get( cursor, - is_readable_by=user.id, + is_readable_by=determine_user_id(user), gs_id=geneset_id, with_publication_info=False, ) @@ -247,14 +253,11 @@ def get_geneset_gene_values( :return: dictionary response (geneset and genset values). """ try: - if user is None or user.id is None: - return {"error": True, "message": message.ACCESS_FORBIDDEN} - ## Check genset exists and user can read it results = db_geneset.get( cursor, gs_id=geneset_id, - is_readable_by=user.id, + is_readable_by=determine_user_id(user), with_publication_info=False, ) if len(results) <= 0: @@ -307,12 +310,9 @@ def get_geneset_w_gene_id_type( @return: Dictionary response (geneset identifier, geneset, and genset values). """ try: - if user is None or user.id is None: - return {"error": True, "message": message.ACCESS_FORBIDDEN} - results = db_geneset.get( cursor, - is_readable_by=user.id, + is_readable_by=determine_user_id(user), gs_id=geneset_id, with_publication_info=False, ) @@ -412,7 +412,10 @@ def update_geneset_threshold( return {"error": True, "message": message.ACCESS_FORBIDDEN} db_threshold.set_geneset_threshold( - cursor=cursor, geneset_id=geneset_id, geneset_score_type=geneset_score + cursor=cursor, + user_id=user.id, + geneset_id=geneset_id, + geneset_score_type=geneset_score ) return {} @@ -438,11 +441,8 @@ def get_geneset_ontology_terms( @return: dictionary response (ontology terms). """ try: - if user is None or user.id is None: - return {"error": True, "message": message.ACCESS_FORBIDDEN} - is_gs_readable = db_geneset.is_readable( - cursor=cursor, user_id=user.id, geneset_id=geneset_id + cursor=cursor, user_id=determine_user_id(user), geneset_id=geneset_id ) if is_gs_readable is False: return {"error": True, "message": message.INACCESSIBLE_OR_FORBIDDEN} From 2333b18f0ce447e403447287cbb6624a5a946f1b Mon Sep 17 00:00:00 2001 From: Alexander Berger Date: Wed, 23 Oct 2024 14:14:07 -0400 Subject: [PATCH 3/9] Fixing formatting and linting --- src/geneweaver/api/controller/genesets.py | 5 ++--- src/geneweaver/api/services/geneset.py | 4 ++-- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/src/geneweaver/api/controller/genesets.py b/src/geneweaver/api/controller/genesets.py index d0a8787..f6f96f2 100644 --- a/src/geneweaver/api/controller/genesets.py +++ b/src/geneweaver/api/controller/genesets.py @@ -5,7 +5,7 @@ from tempfile import TemporaryDirectory from typing import Optional, Set -from fastapi import APIRouter, Depends, HTTPException, Path, Query, Security, Request +from fastapi import APIRouter, Depends, HTTPException, Path, Query, Request, Security from fastapi.responses import FileResponse, StreamingResponse from geneweaver.api import dependencies as deps from geneweaver.api.schemas.apimodels import GeneValueReturn @@ -16,9 +16,8 @@ from geneweaver.core.enum import GeneIdentifier, GenesetTier, Species from geneweaver.core.schema.score import GenesetScoreType, ScoreType from geneweaver.db import search as db_search -from typing_extensions import Annotated - from jax.apiutils import CollectionResponse +from typing_extensions import Annotated from . import message as api_message diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py index 3ee02e2..749f3b5 100644 --- a/src/geneweaver/api/services/geneset.py +++ b/src/geneweaver/api/services/geneset.py @@ -19,7 +19,7 @@ ONTO_GSO_REF_TYPE = "GeneWeaver Primary Annotation" -def determine_user_id(user: Optional[User] = None): +def determine_user_id(user: Optional[User] = None) -> int: """Determine the user ID from the user object. :param user: The user object. @@ -415,7 +415,7 @@ def update_geneset_threshold( cursor=cursor, user_id=user.id, geneset_id=geneset_id, - geneset_score_type=geneset_score + geneset_score_type=geneset_score, ) return {} From 212e6bd109fb5901a16e6cb4e1e3f2e0189c3346 Mon Sep 17 00:00:00 2001 From: Alexander Berger Date: Wed, 23 Oct 2024 14:47:20 -0400 Subject: [PATCH 4/9] Update/fix tests --- tests/services/test_genset.py | 50 ++++++++++++++++++++++----------- tests/services/test_ontology.py | 2 +- 2 files changed, 35 insertions(+), 17 deletions(-) diff --git a/tests/services/test_genset.py b/tests/services/test_genset.py index ead95a9..4d223f3 100644 --- a/tests/services/test_genset.py +++ b/tests/services/test_genset.py @@ -36,13 +36,15 @@ def test_get_geneset(mock_db_geneset, mock_db_genset_value): @patch("geneweaver.api.services.geneset.db_geneset") def test_get_geneset_no_user_access(mock_db_geneset): """Test get geneset by ID with no user access.""" + mock_db_geneset.get.return_value = [] response = geneset.get_geneset(None, 1234, None) - assert response.get("error") is True - assert response.get("message") == message.ACCESS_FORBIDDEN + assert "data" in response + assert response["data"] is None mock_db_geneset.get.return_value = [] response = geneset.get_geneset(None, 1234, mock_user) - assert response.get("data") is None + assert "data" in response + assert response["data"] is None @patch("geneweaver.api.services.geneset.db_geneset") @@ -126,17 +128,28 @@ def test_get_geneset_w_gene_id_type_2_response( ) -def test_get_geneset_w_gene_id_type_no_user(): +@patch("geneweaver.api.services.geneset.db_geneset") +@patch("geneweaver.api.services.geneset.get_gsv_w_gene_homology_update") +def test_get_geneset_w_gene_id_type_no_user(mock_db_geneset, mock_gsv): """Test get_geneset_w_gene_id_type with invalid user.""" + mock_db_geneset.get.return_value = [geneset_by_id_resp.get("geneset")] + mock_gsv.return_value = geneset_by_id_resp.get("geneset_values") + response = geneset.get_geneset_w_gene_id_type(None, 1234, None, GeneIdentifier(2)) - assert response.get("error") is True - assert response.get("message") == message.ACCESS_FORBIDDEN + assert response is not None + assert isinstance(response, dict) + assert "gene_identifier_type" in response + assert "geneset" in response + assert "geneset_values" in response response = geneset.get_geneset_w_gene_id_type( None, 1234, User(id=None), GeneIdentifier(2) ) - assert response.get("error") is True - assert response.get("message") == message.ACCESS_FORBIDDEN + assert response is not None + assert isinstance(response, dict) + assert "gene_identifier_type" in response + assert "geneset" in response + assert "geneset_values" in response @patch("geneweaver.api.services.geneset.db_geneset") @@ -152,17 +165,18 @@ def test_geneset_w_gene_id_type_db_call_error(mock_db_geneset): def test_get_geneset_metadata(mock_db_geneset): """Test get geneset metadata by geneset id.""" mock_db_geneset.get.return_value = [geneset_by_id_resp.get("geneset")] - response = geneset.get_geneset_metadata(None, 1234, mock_user) + response = geneset.get_geneset_metadata(None, 1234, mock_user) + assert "geneset" in response assert response.get("geneset") == geneset_by_id_resp["geneset"] response = geneset.get_geneset_metadata(None, 1234, None) - assert response.get("error") is True - assert response.get("message") == message.ACCESS_FORBIDDEN + assert "geneset" in response + assert response.get("geneset") == geneset_by_id_resp["geneset"] response = geneset.get_geneset_metadata(None, 1234, User(id=None)) - assert response.get("error") is True - assert response.get("message") == message.ACCESS_FORBIDDEN + assert "geneset" in response + assert response.get("geneset") == geneset_by_id_resp["geneset"] @patch("geneweaver.api.services.geneset.db_geneset") @@ -378,14 +392,18 @@ def test_get_geneset_gene_values_db_errors(mock_db_geneset_value): ) +@patch("geneweaver.api.services.geneset.db_geneset.get") @patch("geneweaver.api.services.geneset.db_geneset_value") -def test_get_geneset_gene_values_invalid_user(mock_db_geneset_value): +def test_get_geneset_gene_values_invalid_user( + mock_db_geneset_get, mock_db_geneset_value +): """Test invalid user.""" + mock_db_geneset_get.return_value = [] response = geneset.get_geneset_gene_values( None, user=None, geneset_id=1234, gene_id_type=None ) - assert response.get("error") is True - assert response.get("message") == message.ACCESS_FORBIDDEN + assert "data" in response + assert response["data"] is None @patch("geneweaver.api.services.geneset.db_geneset") diff --git a/tests/services/test_ontology.py b/tests/services/test_ontology.py index 6b907af..c7b947a 100644 --- a/tests/services/test_ontology.py +++ b/tests/services/test_ontology.py @@ -54,7 +54,7 @@ def test_get_geneset_ontology_terms_no_user(mock_db_geneset, mock_db_ontology): response = geneset.get_geneset_ontology_terms(None, 1234, None) - assert response == {"error": True, "message": message.ACCESS_FORBIDDEN} + assert response == {"error": True, "message": message.INACCESSIBLE_OR_FORBIDDEN} @patch("geneweaver.api.services.geneset.db_ontology") From 6244c8edb3ffccf3b4dcd1f1e4cc872ffbd9cb16 Mon Sep 17 00:00:00 2001 From: Alexander Berger Date: Thu, 24 Oct 2024 14:44:26 -0400 Subject: [PATCH 5/9] Updating geneweaver-db dependencies --- poetry.lock | 6 +++--- pyproject.toml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index d6c302c..259abb9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -578,13 +578,13 @@ requests = ">=2.32.0,<3.0.0" [[package]] name = "geneweaver-db" -version = "0.6.0a0" +version = "0.6.0a1" description = "Database Interaction Services for GeneWeaver" optional = false python-versions = "<4.0,>=3.9" files = [ - 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diff --git a/src/geneweaver/api/dependencies.py b/src/geneweaver/api/dependencies.py index 01167b8..26d87c6 100644 --- a/src/geneweaver/api/dependencies.py +++ b/src/geneweaver/api/dependencies.py @@ -77,16 +77,14 @@ def _get_user_details(cursor: Cursor, user: UserInternal) -> UserInternal: :param user: The user object. """ try: - user.id = db_user.by_sso_id_and_email(cursor, user.sso_id, user.email)[0][ - "usr_id" - ] + user.id = db_user.by_sso_id_and_email(cursor, user.sso_id, user.email).id except IndexError as e: if db_user.sso_id_exists(cursor, user.sso_id): raise AuthenticationMismatch( detail="Email and SSO ID Mismatch. Please contact and administrator." ) from e elif db_user.email_exists(cursor, user.email): - user.id = db_user.by_email(cursor, user.email)[0]["usr_id"] + user.id = db_user.by_email(cursor, user.email).id _ = db_user.link_user_id_with_sso_id(cursor, user.id, user.sso_id) else: if not user.name: From 4c5f43d94c0b040bbd76dcf0b9590382187d5d05 Mon Sep 17 00:00:00 2001 From: Alexander Berger Date: Tue, 29 Oct 2024 15:22:59 -0400 Subject: [PATCH 8/9] Fixing permissions on threshold update endpoint --- src/geneweaver/api/services/geneset.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/geneweaver/api/services/geneset.py b/src/geneweaver/api/services/geneset.py index 749f3b5..b1c40ef 100644 --- a/src/geneweaver/api/services/geneset.py +++ b/src/geneweaver/api/services/geneset.py @@ -406,17 +406,17 @@ def update_geneset_threshold( if user is None or user.id is None: return {"error": True, "message": message.ACCESS_FORBIDDEN} - if not db_geneset.user_is_owner( - cursor=cursor, user_id=user.id, geneset_id=geneset_id - ): + try: + db_threshold.set_geneset_threshold( + cursor=cursor, + user_id=user.id, + geneset_id=geneset_id, + geneset_score_type=geneset_score, + ) + + except ValueError: return {"error": True, "message": message.ACCESS_FORBIDDEN} - db_threshold.set_geneset_threshold( - cursor=cursor, - user_id=user.id, - geneset_id=geneset_id, - geneset_score_type=geneset_score, - ) return {} except Exception as err: From 817760b27e7ee0fa9521b15a80eb744146d4cb9b Mon Sep 17 00:00:00 2001 From: Alexander Berger Date: Wed, 30 Oct 2024 07:48:40 -0400 Subject: [PATCH 9/9] Fix geneset threshold test --- tests/services/test_genset.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tests/services/test_genset.py b/tests/services/test_genset.py index 4d223f3..4dda38f 100644 --- a/tests/services/test_genset.py +++ b/tests/services/test_genset.py @@ -429,6 +429,7 @@ def test_geneset_thershold_update_errors(mock_db_threshold, mock_db_geneset): geneset_threshold = GenesetScoreType(**geneset_threshold_update_req) # user is not the geneset owner + mock_db_threshold.set_geneset_threshold.side_effect = ValueError() response = geneset.update_geneset_threshold( cursor=None, user=mock_user, geneset_id=1234, geneset_score=geneset_threshold ) @@ -436,6 +437,7 @@ def test_geneset_thershold_update_errors(mock_db_threshold, mock_db_geneset): assert response.get("message") == message.ACCESS_FORBIDDEN # user is not logged-in + mock_db_threshold.set_geneset_threshold.side_effect = ValueError() response = geneset.update_geneset_threshold( cursor=None, user=None, geneset_id=1234, geneset_score=geneset_threshold )